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Coexpression cluster:C3261: Difference between revisions

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|ontology_enrichment_disease=DOID:162!1.56e-11!235;DOID:14566!6.72e-11!239;DOID:0050686!4.51e-09!137;DOID:2531!1.04e-07!51;DOID:0060083!1.04e-07!51;DOID:0050687!1.72e-07!143;DOID:1240!5.96e-07!39
|ontology_enrichment_disease=DOID:162!1.56e-11!235;DOID:14566!6.72e-11!239;DOID:0050686!4.51e-09!137;DOID:2531!1.04e-07!51;DOID:0060083!1.04e-07!51;DOID:0050687!1.72e-07!143;DOID:1240!5.96e-07!39
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189390848396959!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658940291569899!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323992391537851!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320833579814547!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460500071392484!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00436098083959619!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.015574834333148!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185951472893635!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293452555731279!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268801645441303!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469930356701728!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172459491286278!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156290111605693!ZEB1#6935;2:11.2589546783626:0.0101022267664633:0.0378024529295112!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00388034099250536
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}}
}}

Revision as of 13:44, 5 September 2012


Full id: C3261_CD4_CD8_non_Natural_CD19_CD14_cerebellum



Phase1 CAGE Peaks

Hg19::chr12:133562959..133563013,+p1@ZNF26
Hg19::chr1:70687122..70687136,+p5@SRSF11
Hg19::chr1:70687137..70687200,+p2@SRSF11


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br><br>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell3.97e-29172
angioblastic mesenchymal cell3.97e-29172
hematopoietic cell1.19e-25182
hematopoietic oligopotent progenitor cell1.92e-25165
hematopoietic multipotent progenitor cell1.92e-25165
leukocyte3.43e-23140
hematopoietic lineage restricted progenitor cell1.18e-20124
lymphocyte1.24e-2053
common lymphoid progenitor1.24e-2053
lymphoid lineage restricted progenitor cell1.64e-2052
nongranular leukocyte4.68e-20119
mature alpha-beta T cell4.70e-1118
alpha-beta T cell4.70e-1118
immature T cell4.70e-1118
mature T cell4.70e-1118
immature alpha-beta T cell4.70e-1118
lymphocyte of B lineage4.17e-1024
pro-B cell4.17e-1024
T cell8.39e-1025
pro-T cell8.39e-1025
myeloid cell1.43e-08112
common myeloid progenitor1.43e-08112
B cell2.13e-0814
CD8-positive, alpha-beta T cell1.42e-0711
Disease
Ontology termp-valuen
cancer1.56e-11235
disease of cellular proliferation6.72e-11239
organ system cancer4.51e-09137
hematologic cancer1.04e-0751
immune system cancer1.04e-0751
cell type cancer1.72e-07143
leukemia5.96e-0739


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189390848396959
CHD2#1106310.34402283411690.0009033701102746880.00658940291569899
E2F1#186934.907389214879320.008460985347239390.0323992391537851
E2F6#187635.017155731697390.00791769806886330.0320833579814547
ELF1#199734.258097958807540.01295179875054610.0460500071392484
GATA2#2624312.7449317335540.0004829527704283790.00436098083959619
GTF2B#2959221.29588662288280.002878180589911410.015574834333148
MAX#414936.452555509007120.003721913834265510.0185951472893635
MYC#460935.22228187160940.007020843755740150.0293452555731279
NFKB1#479035.488063424193840.006049381815655430.0268801645441303
NRF1#4899312.21027944771090.0005492172401020010.00469930356701728
PAX5#507936.669565531177830.003370290999677260.0172459491286278
ZBTB33#10009221.10981668665410.002928597060603240.0156290111605693
ZEB1#6935211.25895467836260.01010222676646330.0378024529295112
ZNF143#7702313.50087655222790.0004062804962997170.00388034099250536



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.